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westram 2022-08-03 15:52 Rev.: 19206

* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205

6 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+6 -4)

westram 2022-07-21 14:01 Rev.: 19167

* reintegrates 'split' into 'trunk'
* adds: log:branches/split@19102:19166

15 lines of code changed in 2 files:

• SL/ALILINK: AdminGui.cxx (+8 -14), TranslateRealign.cxx (+7 -6)

westram 2022-06-20 12:03 Rev.: 19061

* fix loop vectorization checks failing with gcc 10.x

1 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+1 -1)

westram 2022-03-04 16:13 Rev.: 18962

* eliminate unused parameter {{{fallback2default}}} from {{{create_option_menu}}}.

4 lines of code changed in 1 file:

• SL/ALILINK: AdminGui.cxx (+4 -4)

westram 2022-03-04 12:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

3 lines of code changed in 1 file:

• SL/ALILINK: Makefile (+3)

westram 2020-10-05 16:26 Rev.: 18600

* copy source alignment name (fixes #829).

4 lines of code changed in 1 file:

• SL/ALILINK: AdminGui.cxx (+4 -3)

westram 2020-10-05 16:24 Rev.: 18599

* fix parameters of {{{GBT_rename_alignment}}} + {{{gbt_rename_alignment_of_item}}}
- rename.
- change to bool.
- callers use bool.

5 lines of code changed in 1 file:

• SL/ALILINK: AdminGui.cxx (+5 -2)

westram 2019-10-08 17:51 Rev.: 18159

* full update from child 'fix' into 'trunk'
- fix item name accessors ({{{GBT_get_name}}} + {{{GBT_get_name_or_description}}})
- add {{{null2empty}}}
* adds: log:branches/fix@18140:18158

1 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+1 -1)

westram 2019-07-17 16:22 Rev.: 17980

* use security objects instead of manually calling GB_push/pop_my_security.
* eliminate GB_push/pop_my_security.
* fix scoping using a TA object.

3 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+3 -4)

westram 2019-03-31 11:48 Rev.: 17712

* remove test stub from ALILINK.

0 lines of code changed in 3 files:

• SL/ALILINK: AliAdmin.cxx (new), Makefile (-1)

westram 2018-10-31 10:52 Rev.: 17593

* reintegrates 'fix' into 'trunk'
- performs #798
* adds genetic code tables (24-31)
* adds combined amino acid J (I or L)
* improved translate and/or realign
- handle optional start-/stop-codons
- improve recognition of nuc-triples containing IUPAC-codes
* error messages now always list EMBL table numbers
* adds:
- log:branches/fix@17480:17485,17491:17492,17494:17507,17509:17528,17534:17592
- log:branches/optional@17481:17568

67 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+67 -15)

westram 2018-10-24 15:58 Rev.: 17534

* partial merge from 'fix' into 'trunk'
- globally define what are "gaps"
- kept behavioral changes to a minimum:
* defaults for (user-defined) gap-definition in EDIT4 changed
* EDIT sequence search also uses user-defined gaps
* adds: log:branches/fix@17529:17533

3 lines of code changed in 2 files:

• SL/ALILINK: Makefile (+1), TranslateRealign.cxx (+2 -1)

westram 2018-10-23 10:36 Rev.: 17510

* partial merge from 'fix' into 'trunk'
* adds: [17508/branches/fix]

13 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+13 -13)

westram 2018-05-04 18:06 Rev.: 16986

* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

3 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+3 -3)

westram 2017-11-28 19:22 Rev.: 16766

* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

14 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+14 -19)

westram 2017-11-28 18:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

79 lines of code changed in 3 files:

• SL/ALILINK: AdminGui.cxx (+4 -4), AliAdmin.h (+6 -6), TranslateRealign.cxx (+69 -69)

westram 2017-11-19 16:19 Rev.: 16683

* full update from child 'gcc' into 'trunk'
- more warning fixes
- fix bug in prettyprint
* adds: log:branches/gcc@16668:16682

1 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+1 -1)

westram 2017-11-06 14:54 Rev.: 16628

* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

1 lines of code changed in 1 file:

• SL/ALILINK: TranslateRealign.cxx (+1 -1)

westram 2017-10-27 19:04 Rev.: 16576

* painful merge from 'alilink' into 'trunk'
- attempt to eliminate existing conflicts by merging log:branches/alilink@12782,12786:12787 (=creation of conflicting files)
- also merged back already resolved conflicts (done in alilink)
- a dozen of manual merges :-(
* adds: log:branches/alilink@12782,12786:12787,13999,14004

1837 lines of code changed in 5 files:

• SL/ALILINK: Makefile (+31), TranslateRealign.cxx (new 1780), TranslateRealign.h (new 25), needs_libs (new)

westram 2017-10-08 15:54 Rev.: 16508

* reintegrates 'macros' into 'trunk'
- introduce generic input prompt (related #179)
- use it instead of locally generated windows:
* species (rename + create)
* alignment (rename, copy + create)
* experiments (rename, copy + create)
* genes (rename, copy + extract)
* mergetool (rename SAI + configs)
* SAIviz color translation (copy + create)
- fixed bugs in mergetool ([16503],[16504])
* adds: log:branches/macros@16484:16507

27 lines of code changed in 4 files:

• SL/ALILINK: AdminGui.cxx (+26 -77), AliAdmin.h (-3), Makefile (+1)

westram 2016-08-11 11:05 Rev.: 15176

* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

1 lines of code changed in 1 file:

• SL/ALILINK: Makefile (+1)

westram 2016-04-16 14:52 Rev.: 14731

* mark code binding callbacks to non-button-widgets (probably incomplete; see #559 for details)

4 lines of code changed in 1 file:

• SL/ALILINK: AdminGui.cxx (+4 -4)

westram 2015-11-04 10:57 Rev.: 14453

* do not cast AW_POPDOWN

5 lines of code changed in 1 file:

• SL/ALILINK: AdminGui.cxx (+5 -5)

westram 2015-01-23 15:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 2 files:

• SL/ALILINK: Makefile (+1 -1)

westram 2014-08-14 12:18 Rev.: 12757

* unify selectionlist creator names
* awt_create_selection_list_on_pt_servers
- remove param 'popup', instead split into two function (button and list) as done for SAIs

1 lines of code changed in 2 files:

• SL/ALILINK: AdminGui.cxx (new)